Mutagenetix > Incidental Mutation

Incidental Mutation 'R2520:Nanog'

254342

Institutional Source

Beutler Lab

Gene Symbol

Nanog

Ensembl Gene

ENSMUSG00000012396

Gene Name

Nanog homeobox

Synonyms

ENK, 2410002E02Rik, ecat4

MMRRC Submission

040424-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2520 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

122684448-122691592 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 122690418 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 249 (N249K)

Ref Sequence

ENSEMBL: ENSMUSP00000108200 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000012540] [ENSMUST00000112580] [ENSMUST00000112581]

AlphaFold

Q80Z64

Predicted Effect

probably benign
Transcript: ENSMUST00000012540
AA Change: N274K

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000012540
Gene: ENSMUSG00000012396
AA Change: N274K

Domain	Start	End	E-Value	Type
low complexity region	13	25	N/A	INTRINSIC
HOX	96	158	5.33e-22	SMART
low complexity region	206	230	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000112580
AA Change: N249K

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000108199
Gene: ENSMUSG00000012396
AA Change: N249K

Domain	Start	End	E-Value	Type
HOX	71	133	5.33e-22	SMART
low complexity region	181	205	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000112581
AA Change: N249K

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000108200
Gene: ENSMUSG00000012396
AA Change: N249K

Domain	Start	End	E-Value	Type
HOX	71	133	5.33e-22	SMART
low complexity region	181	205	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.1%

Validation Efficiency

MGI Phenotype

FUNCTION: The protein encoded by this gene is a DNA binding homeobox transcription factor involved in embryonic stem (ES) cell proliferation, renewal, and pluripotency. The encoded protein can block ES cell differentiation and can also autorepress its own expression in differentiating cells. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mice homozygous for a disruption in this gene die between E3.5 and E5.5 with abnormal embryonic and extraembryonic tissue development. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700109H08Rik	A	T	5: 3,625,773 (GRCm39)	N70I	probably damaging	Het
4930503B20Rik	G	A	3: 146,356,261 (GRCm39)	R216W	probably damaging	Het
Abcb9	C	T	5: 124,218,091 (GRCm39)		probably null	Het
Arhgdia	A	T	11: 120,470,852 (GRCm39)	V72E	probably damaging	Het
Arsb	A	T	13: 94,077,207 (GRCm39)	K525*	probably null	Het
Bckdha	A	C	7: 25,341,124 (GRCm39)	I79S	probably benign	Het
Carm1	G	A	9: 21,494,893 (GRCm39)		probably null	Het
Cers5	G	A	15: 99,634,262 (GRCm39)	T362I	probably damaging	Het
Clec4b2	T	A	6: 123,177,942 (GRCm39)	F86I	probably damaging	Het
Crispld1	G	A	1: 17,821,000 (GRCm39)	D347N	probably damaging	Het
Csf3r	A	T	4: 125,929,145 (GRCm39)	T352S	probably benign	Het
Daam2	G	A	17: 49,787,785 (GRCm39)	Q443*	probably null	Het
Dcbld1	A	G	10: 52,195,641 (GRCm39)	D283G	probably damaging	Het
Dpp9	T	C	17: 56,513,868 (GRCm39)	E82G	probably damaging	Het
Dync1li1	A	G	9: 114,518,074 (GRCm39)	D42G	probably null	Het
Eml6	T	C	11: 29,741,993 (GRCm39)	H1130R	probably damaging	Het
Enox1	A	T	14: 77,819,839 (GRCm39)	Y198F	probably damaging	Het
Epop	A	G	11: 97,519,554 (GRCm39)	L185P	probably benign	Het
Frem1	A	T	4: 82,868,527 (GRCm39)	C1485S	probably damaging	Het
Gbf1	T	A	19: 46,253,806 (GRCm39)	S571T	probably benign	Het
Gm5965	A	T	16: 88,575,414 (GRCm39)	I196F	probably null	Het
Gm8237	T	A	14: 5,863,642 (GRCm38)	I8L	possibly damaging	Het
Gria2	A	C	3: 80,614,269 (GRCm39)	N590K	probably damaging	Het
Hectd2	T	A	19: 36,589,633 (GRCm39)		probably null	Het
Hmcn1	T	A	1: 150,619,398 (GRCm39)	T1239S	possibly damaging	Het
Hps3	A	T	3: 20,083,194 (GRCm39)	D167E	probably damaging	Het
Htr1a	A	G	13: 105,581,881 (GRCm39)	S374G	probably benign	Het
Il16	C	T	7: 83,301,202 (GRCm39)	G307S	probably benign	Het
Ipmk	T	C	10: 71,217,047 (GRCm39)	F198S	probably damaging	Het
Lyz2	T	A	10: 117,114,558 (GRCm39)	I124F	probably damaging	Het
Maea	T	C	5: 33,515,854 (GRCm39)	V47A	probably damaging	Het
Mrc2	G	A	11: 105,239,257 (GRCm39)		probably null	Het
Mrgpra1	A	T	7: 46,985,020 (GRCm39)	C220S	possibly damaging	Het
Myo5c	A	T	9: 75,204,931 (GRCm39)	K1595*	probably null	Het
Naga	G	T	15: 82,214,295 (GRCm39)	D405E	probably benign	Het
Nhlh1	G	T	1: 171,881,570 (GRCm39)	R99S	probably damaging	Het
Ntrk2	T	A	13: 59,202,090 (GRCm39)		probably null	Het
Nudt2	A	G	4: 41,480,354 (GRCm39)	E79G	probably benign	Het
Or2ad1	A	T	13: 21,326,746 (GRCm39)	C160*	probably null	Het
Or4f60	A	T	2: 111,902,013 (GRCm39)	M305K	probably benign	Het
Or52n2	T	A	7: 104,542,080 (GRCm39)	I252F	probably benign	Het
Pitpnm2	T	C	5: 124,267,464 (GRCm39)	D592G	probably damaging	Het
Prps1l3	T	C	12: 57,285,369 (GRCm39)	V53A	probably damaging	Het
Psmd2	T	G	16: 20,481,826 (GRCm39)	V853G	probably damaging	Het
Pycard	A	G	7: 127,592,677 (GRCm39)	I50T	possibly damaging	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Rnf168	T	A	16: 32,097,221 (GRCm39)	S99T	probably benign	Het
Rph3al	A	G	11: 75,797,373 (GRCm39)	S108P	possibly damaging	Het
Sdk1	G	A	5: 142,071,526 (GRCm39)	A979T	probably benign	Het
Sec16a	G	A	2: 26,331,368 (GRCm39)	Q216*	probably null	Het
Slc35f3	T	A	8: 127,121,312 (GRCm39)	V391E	possibly damaging	Het
Slf1	T	A	13: 77,199,384 (GRCm39)	I666F	probably damaging	Het
Slfn14	A	G	11: 83,167,013 (GRCm39)	V834A	probably damaging	Het
Tab2	G	A	10: 7,783,245 (GRCm39)	P679L	probably damaging	Het
Tbc1d10b	A	G	7: 126,799,455 (GRCm39)		probably null	Het
Tmeff1	T	A	4: 48,604,679 (GRCm39)	C91S	probably damaging	Het
Tmem108	G	T	9: 103,366,481 (GRCm39)	N503K	possibly damaging	Het
Trbv28	A	G	6: 41,248,541 (GRCm39)	T24A	probably damaging	Het
Trim34b	A	G	7: 103,980,446 (GRCm39)	E178G	probably damaging	Het
Trmt1l	T	A	1: 151,329,696 (GRCm39)	H546Q	probably benign	Het
Ttc39d	A	G	17: 80,523,799 (GRCm39)	I153V	probably benign	Het
Ttll13	T	C	7: 79,899,964 (GRCm39)	V101A	probably damaging	Het
Ubash3b	A	T	9: 40,926,243 (GRCm39)	H501Q	probably damaging	Het
Upf3a	T	A	8: 13,846,443 (GRCm39)		probably null	Het
Usp48	A	G	4: 137,352,562 (GRCm39)	S94G	probably benign	Het
Wdr86	T	C	5: 24,917,573 (GRCm39)	*381W	probably null	Het
Wdr90	G	A	17: 26,074,326 (GRCm39)	P680S	probably damaging	Het
Zbtb22	G	A	17: 34,135,956 (GRCm39)	V34M	probably damaging	Het
Zbtb8a	A	G	4: 129,253,689 (GRCm39)		probably null	Het
Zfhx4	C	T	3: 5,468,418 (GRCm39)	P2859S	probably benign	Het
Zfp512b	A	G	2: 181,231,295 (GRCm39)	V295A	probably damaging	Het
Zfp608	A	T	18: 55,121,578 (GRCm39)	V3E	possibly damaging	Het
Zfp748	G	T	13: 67,694,781 (GRCm39)	D32E	possibly damaging	Het

Other mutations in Nanog

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00475:Nanog	APN	6	122,688,495 (GRCm39)	critical splice acceptor site	probably null
IGL03278:Nanog	APN	6	122,688,704 (GRCm39)	missense	probably damaging	1.00
IGL03387:Nanog	APN	6	122,688,731 (GRCm39)	missense	probably damaging	1.00
R0280:Nanog	UTSW	6	122,690,357 (GRCm39)	missense	probably damaging	0.96
R1443:Nanog	UTSW	6	122,688,734 (GRCm39)	missense	probably damaging	1.00
R3037:Nanog	UTSW	6	122,690,227 (GRCm39)	missense	possibly damaging	0.81
R4486:Nanog	UTSW	6	122,689,676 (GRCm39)	critical splice donor site	probably null
R4770:Nanog	UTSW	6	122,688,550 (GRCm39)	missense	possibly damaging	0.63
R4790:Nanog	UTSW	6	122,684,874 (GRCm39)	missense	probably benign	0.00
R4825:Nanog	UTSW	6	122,690,299 (GRCm39)	missense	probably benign	0.09
R4931:Nanog	UTSW	6	122,684,865 (GRCm39)	missense	possibly damaging	0.95
R6010:Nanog	UTSW	6	122,690,255 (GRCm39)	missense	probably benign	0.16
R6025:Nanog	UTSW	6	122,690,350 (GRCm39)	missense	possibly damaging	0.94
R7661:Nanog	UTSW	6	122,690,431 (GRCm39)	missense	probably damaging	0.96
R8236:Nanog	UTSW	6	122,690,131 (GRCm39)	missense	probably benign
R8272:Nanog	UTSW	6	122,688,736 (GRCm39)	missense	probably benign	0.00
R8520:Nanog	UTSW	6	122,690,475 (GRCm39)	missense	possibly damaging	0.94
R9500:Nanog	UTSW	6	122,690,219 (GRCm39)	missense	probably damaging	1.00
R9632:Nanog	UTSW	6	122,684,799 (GRCm39)	missense	probably benign	0.00
R9710:Nanog	UTSW	6	122,684,799 (GRCm39)	missense	probably benign	0.00
X0065:Nanog	UTSW	6	122,684,752 (GRCm39)	missense	probably benign
Z1176:Nanog	UTSW	6	122,690,190 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- TGGACCAACCCAACTTGGAA -3'
(R):5'- CTCCAAAGCCTAGAGTTAACACTAAA -3'

Sequencing Primer
(F):5'- GGAACAACCAGACCTGGA -3'
(R):5'- TGCAGAGAAACCCTGTCTTG -3'

Posted On

2014-12-04